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TMExplorer

A Collection of Tumour Microenvironment Single-cell RNA Sequencing Datasets and Corresponding Metadata

Bioconductor version: Release (3.17)

This package provides a tool to search and download a collection of tumour microenvironment single-cell RNA sequencing datasets and their metadata. TMExplorer aims to act as a single point of entry for users looking to study the tumour microenvironment at the single cell level. Users can quickly search available datasets using the metadata table and then download the ones they are interested in for analysis.

Author: Erik Christensen [aut, cre], Alaine Naidas [aut], David Chen [aut], Parisa Shooshtari [aut]

Maintainer: Erik Christensen <echris3 at uwo.ca>

Citation (from within R, enter citation("TMExplorer")):

Installation

To install this package, start R (version "4.3") and enter: 

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("TMExplorer")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("TMExplorer")
TMExplorer HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews CancerData, ExperimentData, ExpressionData, GEO, PackageTypeData, RNASeqData, SequencingData, SingleCellData
Version 1.10.0
License Artistic-2.0
Depends R (>= 4.1), SingleCellExperiment, BiocFileCache
Imports methods, Matrix
Linking To
Suggests BiocStyle, knitr, rmarkdown
System Requirements
Enhances
URL
Bug Reports https://github.com/shooshtarilab/TMExplorer/issues
See More
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package TMExplorer_1.10.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/TMExplorer
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/TMExplorer
Package Short Url https://bioconductor.org/packages/TMExplorer/
Package Downloads Report Download Stats